How are you importing the text from the other program? Are you copy/pasting or…? If copy/paste, are you using “paste and match style” option, or do you specifically want to keep original formatting?
If I’m not misunderstanding what you’re doing/seeing, it sounds like the style from your other program is being pulled into Scrivener and causing the mismatch between Scrivener’s style and what you’re bringing in. If you don’t care to keep original formatting, “paste and match style” is better option.
These may also help, if you want to change the default styles of your project so that when you “paste and match style”, it’ll be pasting in the format you want:
[url]How do you set default indents, font etc for all documents?]
[url]How do I set font and format defaults?]